On cherche à étudier l’effet de trois facteurs sur le transcriptome des racines d’Arabidopsis thaliana. Le CO2, au cours des études préliminaires, s’est montré peu influent en conditions contrôles de fer et de nitrates, et accentué en cas de stress nutritionnel. Nous reprennons ces résultats avec des fonctions génériques et propres pour en faire le résumé et de jolis graphes.

Import des données : matrice d’expression

On a, pour chaque gène et chaque condition, son niveau d’expression en sortie de quantification. On labelle les conditions avec le code suivant : lettre majuscule pour le niveau fort, minuscule pour le niveau faible. Le réplicat est donné après l’underscore.

[1] "cnF_3"
[1] At_AmbientCO2_LowNitrate_Fe1
48 Levels: At_AmbientCO2_HighNitrate_Fe1 ... Sl_ElevatedCO2_LowNitrate_FeStarvation3
[1] "At_AmbientCO2_LowNitrate_Fe"
          cNF_3 cNF_2 cNF_1 cnF_2 cnF_1 cnF_3 CNF_1 CnF_2 CnF_1 CnF_3 cNf_1
AT1G01010  1526  1006  1116  1275   967  1018   854  1132  1294  1364  2325
AT1G01020   416   285   289   349   364   370   226   513   502   561   461
AT1G01030    31    15    19    29    36    28    12    47    34    47    18
          cnf_2 cnf_1 cNf_2 cNf_3 cnf_3 Cnf_3 CNf_1 Cnf_1 Cnf_2 CNf_3 CNf_2
AT1G01010  2113  2193  2564  2364  2074  1987  2027  1754  1697  1537  1898
AT1G01020   407   432   614   380   502   484   467   426   415   413   462
AT1G01030    40    32    44    37    27    42    39    36    40    37    37
          CNF_3 CNF_2
AT1G01010   816   912
AT1G01020   223   312
AT1G01030    15    19
 [ reached 'max' / getOption("max.print") -- omitted 3 rows ]
[1] 23342    24

Effet CO2 en conditions contrôle

On définit les conditions contrôle comme suit : fort nitrate et fort fer.

  (Intercept) groupCNF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "CNF_1" "CNF_3" "CNF_2"
    cNF_3     cNF_2     cNF_1     CNF_1     CNF_3     CNF_2 
1.0090325 1.0047763 0.9805842 1.0116521 0.9699686 1.0239863 

[1] "68  genes DE"

[1] 17

ensembl_gene_id description external_gene_name entrezgene_id
AT1G01060 LHY1 [Source:UniProtKB/TrEMBL;Acc:A0A178W761] LHY 839341
AT1G01560 Mitogen-activated protein kinase 11 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMM5] MPK11 839523
AT1G01680 U-box domain-containing protein 54 [Source:UniProtKB/Swiss-Prot;Acc:Q9LQ92] PUB54 839251
AT1G05880 Probable E3 ubiquitin-protein ligase ARI12 [Source:UniProtKB/Swiss-Prot;Acc:Q84RQ9] ARI12 837098
AT1G08090 High-affinity nitrate transporter 2.1 [Source:UniProtKB/Swiss-Prot;Acc:O82811] NRT2.1 837327
AT1G12805 Nucleotide binding protein [Source:UniProtKB/TrEMBL;Acc:Q3EDD5] 2745749
AT1G14550 Peroxidase 5 [Source:UniProtKB/Swiss-Prot;Acc:Q9M9Q9] PER5 838017
AT1G19250 Probable flavin-containing monooxygenase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMA1] FMO1 838508
AT1G21240 Wall-associated receptor kinase 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMN8] WAK3 838719
AT1G43800 Stearoyl-[acyl-carrier-protein] 9-desaturase 6, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:Q84VY3] S-ACP-DES6 840977
AT1G44030 Cysteine/Histidine-rich C1 domain family protein [Source:TAIR;Acc:AT1G44030] 841003
AT1G51900 Regulator of Vps4 activity in the MVB pathway protein [Source:UniProtKB/TrEMBL;Acc:F4IB75] 841617
AT1G55790 Domain of unknown function (DUF2431) [Source:TAIR;Acc:AT1G55790] NA
AT1G61480 G-type lectin S-receptor-like serine/threonine-protein kinase At1g61480 [Source:UniProtKB/Swiss-Prot;Acc:O64771] 842442
AT1G62510 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9SXE6] 842548
AT1G64170 Cation/H(+) antiporter 16 [Source:UniProtKB/Swiss-Prot;Acc:Q1HDT3] CHX16 842721
AT1G64770 NDH-dependent cyclic electron flow 1 [Source:UniProtKB/TrEMBL;Acc:F4I890] NDF2 842785
AT1G67270 Zinc-finger domain of monoamine-oxidase A repressor R1 protein [Source:TAIR;Acc:AT1G67270] 843047
AT1G73120 At1g73120 [Source:UniProtKB/TrEMBL;Acc:Q9CAS9] 843643
AT1G76930 extensin 4 [Source:TAIR;Acc:AT1G76930] ATEXT4 NA
AT2G01520 MLP-like protein 328 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZVF3] MLP328 814681
AT2G02010 glutamate decarboxylase 4 [Source:TAIR;Acc:AT2G02010] GAD4 814732
AT2G02950 Protein PHYTOCHROME KINASE SUBSTRATE 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9SWI1] PKS1 814823
AT2G26040 Abscisic acid receptor PYL2 [Source:UniProtKB/Swiss-Prot;Acc:O80992] PYL2 817145
AT2G35980 NDR1/HIN1-like protein 10 [Source:UniProtKB/Swiss-Prot;Acc:Q9SJ52] NHL10 818171
AT2G39040 Peroxidase 24 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZV04] PER24 818490
AT2G45760 BON1-associated protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q58FX0] BAP2 819184
AT3G03270 AT3G03270 protein [Source:UniProtKB/TrEMBL;Acc:Q8LFK2] 821303
AT3G07650 COL9 [Source:UniProtKB/TrEMBL;Acc:A0A384KVH3] COL9 819956
AT3G08040 Protein DETOXIFICATION 43 [Source:UniProtKB/Swiss-Prot;Acc:Q9SFB0] DTX43 819995
AT3G08970 TMS1 [Source:UniProtKB/TrEMBL;Acc:A0A178VJB6] ERDJ3A 820049
AT3G12900 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9LE86] 820473
AT3G27650 LOB domain-containing protein 25 [Source:UniProtKB/Swiss-Prot;Acc:Q8L8Q3] LBD25 822387
AT3G53150 UDP-glucosyl transferase 73D1 [Source:TAIR;Acc:AT3G53150] UGT73D1 NA
AT3G53280 Cytochrome P450 71B5 [Source:UniProtKB/Swiss-Prot;Acc:O65784] CYP71B5 824495
AT3G56290 Potassium transporter [Source:UniProtKB/TrEMBL;Acc:Q9LYL4] 824796
AT3G63380 Calcium-transporting ATPase [Source:UniProtKB/TrEMBL;Acc:A0A178VEV7] ACA12 825513
AT4G02330 Probable pectinesterase/pectinesterase inhibitor 41 [Source:UniProtKB/Swiss-Prot;Acc:Q8RXK7] PME41 828064
AT4G10500 Protein DMR6-LIKE OXYGENASE 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZSA8] DLO1 826642
AT4G10510 Subtilisin-like protease SBT3.7 [Source:UniProtKB/Swiss-Prot;Acc:Q9SZY2] SBT3.7 826643
AT4G11170 Putative disease resistance protein At4g11170 [Source:UniProtKB/Swiss-Prot;Acc:O82500] 826718
AT4G11340 Disease resistance protein (TIR-NBS-LRR class) family [Source:UniProtKB/TrEMBL;Acc:Q9SUS7] 826736
AT4G12550 Putative lipid-binding protein AIR1 [Source:UniProtKB/Swiss-Prot;Acc:Q9S7I2] AIR1 826868
AT4G14368 Regulator of chromosome condensation (RCC1) family protein [Source:UniProtKB/TrEMBL;Acc:F4JVE8] 7922506
AT4G14370 Disease resistance protein (TIR-NBS-LRR class) family [Source:TAIR;Acc:AT4G14370] 827081
AT4G15248 B-box domain protein 30 [Source:UniProtKB/Swiss-Prot;Acc:Q1G3I2] MIP1A 3769879
AT4G21380 Receptor-like serine/threonine-protein kinase SD1-8 [Source:UniProtKB/Swiss-Prot;Acc:O81905] SD18 827890
AT4G25100 Superoxide dismutase [Fe] 1, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:P21276] FSD1 828613
AT4G25480 Dehydration-responsive element-binding protein 1A [Source:UniProtKB/Swiss-Prot;Acc:Q9M0L0] DREB1A 828652
AT4G31940 Cytochrome P450 82C4 [Source:UniProtKB/Swiss-Prot;Acc:Q9SZ46] CYP82C4 829324
AT4G33560 At4g33560 [Source:UniProtKB/TrEMBL;Acc:O81873] 829495
AT4G33720 AT4g33720/T16L1_210 [Source:UniProtKB/TrEMBL;Acc:O81888] 829514
AT4G33980 BEST Arabidopsis thaliana protein match is: cold regulated gene 27 (TAIR:AT5G42900.2); Ha. [Source:TAIR;Acc:AT4G33980] 829544
AT4G37060 PATATIN-like protein 5 [Source:TAIR;Acc:AT4G37060] PLP5 829860
AT4G38420 Putative pectinesterase [Source:UniProtKB/TrEMBL;Acc:Q8VYB3] sks9 829999
AT5G02780 Glutathione S-transferase L1 [Source:UniProtKB/Swiss-Prot;Acc:Q6NLB0] GSTL1 831800
AT5G22910 Cation/H(+) antiporter 9 [Source:UniProtKB/Swiss-Prot;Acc:Q9FFB7] CHX9 832355
AT5G23980 Ferric reduction oxidase 4 [Source:UniProtKB/Swiss-Prot;Acc:Q8W110] FRO4 832463
AT5G23990 ferric reduction oxidase 5 [Source:TAIR;Acc:AT5G23990] ATFRO5 832464
AT5G26920 Calmodulin-binding protein 60 G [Source:UniProtKB/Swiss-Prot;Acc:F4K2R6] CBP60G 832750
AT5G39580 Peroxidase 62 [Source:UniProtKB/Swiss-Prot;Acc:Q9FKA4] PER62 833954
AT5G39890 Plant cysteine oxidase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q8LGJ5] PCO2 833986
AT5G44110 ABC transporter I family member 21 [Source:UniProtKB/Swiss-Prot;Acc:Q9XF19] ABCI21 834434
AT5G44190 Transcription activator GLK2 [Source:UniProtKB/Swiss-Prot;Acc:Q9FFH0] GLK2 834442
AT5G56080 NAS2 [Source:UniProtKB/TrEMBL;Acc:A0A178ULG9] NAS2 835707
AT5G59520 Zinc transporter 2 [Source:UniProtKB/Swiss-Prot;Acc:Q9LTH9] ZIP2 836071
AT5G60100 Pseudo-response regulator 3 [Source:UniProtKB/TrEMBL;Acc:F4JXG7] PRR3 836132
AT5G64120 Peroxidase [Source:UniProtKB/TrEMBL;Acc:A0A178UAR8] PER71 836533
# Low nitrate
  (Intercept) groupCnF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cnF_2" "cnF_1" "cnF_3" "CnF_2" "CnF_1" "CnF_3"
    cnF_2     cnF_1     cnF_3     CnF_2     CnF_1     CnF_3 
0.9862253 0.9873030 0.9924054 1.0167225 1.0047221 1.0126218 

[1] "1312  genes DE"

Low iron

  (Intercept) groupCNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNf_1" "cNf_2" "cNf_3" "CNf_1" "CNf_3" "CNf_2"
    cNf_1     cNf_2     cNf_3     CNf_1     CNf_3     CNf_2 
0.9799002 1.0044883 0.9723876 0.9981139 1.0241404 1.0209697 

[1] "2219  genes DE"

Low iron and nitrate

  (Intercept) groupCnf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cnf_2" "cnf_1" "cnf_3" "Cnf_3" "Cnf_1" "Cnf_2"
    cnf_2     cnf_1     cnf_3     Cnf_3     Cnf_1     Cnf_2 
0.9975633 1.0046643 1.0015093 0.9727479 1.0064673 1.0170479 

[1] "1656  genes DE"

Venn diagram

On visualise les gènes différentiellement exprimés en commun entre les différents niveaux des autres facteurs.

    gene_id   a.value    m.value      p.value      q.value rank estimatedDEG
1 AT5G64120  8.797218 -1.1121447 1.896207e-15 4.426127e-11    1            1
2 AT1G19250  9.948535 -0.8706103 1.978583e-14 1.947526e-10    2            1
3 AT4G25100  9.324940 -0.9038503 2.503032e-14 1.947526e-10    3            1
4 AT5G59520  8.819711 -1.2066060 1.693750e-12 9.063158e-09    4            1
5 AT2G01520 14.038784 -0.9716064 1.941384e-12 9.063158e-09    5            1
6 AT1G67270  5.104540 -2.2140173 3.332071e-12 1.296287e-08    6            1
7 AT5G23980  8.719121 -1.1156310 2.015065e-10 6.719378e-07    7            1
8 AT4G37060 10.229806 -0.8191550 6.993735e-10 2.040597e-06    8            1
9 AT5G23990  4.823373 -2.0335514 9.572232e-10 2.482612e-06    9            1
  upreg
1     0
2     0
3     0
4     0
5     0
6     0
7     0
8     0
9     0
 [ reached 'max' / getOption("max.print") -- omitted 59 rows ]
    gene_id   a.value   m.value      p.value      q.value rank estimatedDEG
1 AT5G61600 10.978022  1.715345 5.768501e-56 1.346484e-51    1            1
2 AT4G27450 10.987889  1.361106 1.241560e-51 1.449024e-47    2            1
3 AT1G27730  9.421760  2.187544 2.462590e-51 1.916059e-47    3            1
4 AT5G51190  8.417337  2.782680 4.320997e-49 2.521518e-45    4            1
5 AT2G27830  9.879502  1.316552 1.397834e-39 6.525650e-36    5            1
6 AT1G19530 12.542251  1.538979 1.842265e-38 7.167027e-35    6            1
7 AT4G27280 10.488397  1.691216 4.608884e-38 1.536865e-34    7            1
8 AT5G13930 10.407278 -1.747350 6.719526e-38 1.960590e-34    8            1
9 AT3G44260  8.737846  2.483672 1.820216e-36 4.720832e-33    9            1
  upreg
1     1
2     1
3     1
4     1
5     1
6     1
7     1
8     0
9     1
 [ reached 'max' / getOption("max.print") -- omitted 1303 rows ]
    gene_id   a.value   m.value       p.value       q.value rank estimatedDEG
1 AT1G78340 10.002535 -3.261719 5.399049e-136 1.260246e-131    1            1
2 AT4G13180 10.301728 -2.811270 3.011796e-121 3.515067e-117    2            1
3 AT4G15550  8.217350 -3.781600 5.522983e-117 4.297249e-113    3            1
4 AT4G34131  8.946763 -2.699004  1.584031e-95  9.243612e-92    4            1
5 AT1G76680  9.778808 -3.051667  2.789158e-90  1.302091e-86    5            1
6 AT3G28345  9.654586 -2.538451  3.170729e-89  1.233519e-85    6            1
7 AT3G45060  9.161753  2.510301  5.415418e-82  1.805810e-78    7            1
8 AT1G76690  9.762616 -2.235867  5.461401e-76  1.593500e-72    8            1
9 AT3G28740  4.011621 -7.093650  9.075419e-76  2.353760e-72    9            1
  upreg
1     0
2     0
3     0
4     0
5     0
6     0
7     1
8     0
9     0
 [ reached 'max' / getOption("max.print") -- omitted 2210 rows ]
    gene_id   a.value   m.value      p.value      q.value rank estimatedDEG
1 AT3G49620  8.971142  3.325629 4.576332e-77 1.068207e-72    1            1
2 AT2G26400 12.032573 -2.107176 1.946526e-64 2.271791e-60    2            1
3 AT1G21100  9.986600  1.996729 3.562033e-43 2.771499e-39    3            1
4 AT1G69530  9.527594 -1.507353 2.066807e-40 1.206085e-36    4            1
5 AT5G51860  6.042441  3.573607 4.906245e-40 2.290431e-36    5            1
6 AT5G51870  8.032896  1.826646 6.948595e-39 2.703235e-35    6            1
7 AT1G08630  8.692334  2.049414 1.918515e-37 6.397426e-34    7            1
8 AT1G56600  8.952644 -1.850385 1.108793e-36 3.235181e-33    8            1
9 AT1G43800 11.887403 -2.934754 2.086789e-36 5.412203e-33    9            1
  upreg
1     1
2     0
3     1
4     0
5     1
6     1
7     1
8     0
9     0
 [ reached 'max' / getOption("max.print") -- omitted 1647 rows ]

   ensembl_gene_id
1        AT1G02640
2        AT1G11185
3        AT1G11260
4        AT1G11920
5        AT1G12040
6        AT1G12805
7        AT1G17180
8        AT1G18400
9        AT1G19250
10       AT1G27950
11       AT1G29100
12       AT1G33055
13       AT1G43800
14       AT1G48930
15       AT1G54950
16       AT1G54970
17       AT1G55790
18       AT1G56580
                                                                                                                                                                                                                                            description
1                                                                                                                                                                                 Probable beta-D-xylosidase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q94KD8]
2                                                                                                                                                                                                                 other RNA [Source:TAIR;Acc:AT1G11185]
3                                                                                                                                                                                                         STP1 [Source:UniProtKB/TrEMBL;Acc:A0A178WJ63]
4                                                                                                                                                                                     Putative pectate lyase 2 [Source:UniProtKB/Swiss-Prot;Acc:O65388]
5                                                                                                                                                                  Leucine-rich repeat extensin-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:O65375]
6                                                                                                                                                                                       Nucleotide binding protein [Source:UniProtKB/TrEMBL;Acc:Q3EDD5]
7                                                                                                                                                                                Glutathione S-transferase U25 [Source:UniProtKB/Swiss-Prot;Acc:Q9SHH7]
8                                                                                                                                                                                   Transcription factor BEE 1 [Source:UniProtKB/Swiss-Prot;Acc:Q8GZ13]
9                                                                                                                                                                   Probable flavin-containing monooxygenase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMA1]
10                                                                                                                                                          Non-specific lipid transfer protein GPI-anchored 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9C7F7]
11                                                                                                                                                                 Heavy metal transport/detoxification superfamily protein [Source:TAIR;Acc:AT1G29100]
12                                                                                                                                              Uncharacterized protein unannotated coding sequence from BAC F9L11 [Source:UniProtKB/TrEMBL;Acc:Q94K21]
13                                                                                                                                               Stearoyl-[acyl-carrier-protein] 9-desaturase 6, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:Q84VY3]
14                                                                                                                                                                                             Endoglucanase 5 [Source:UniProtKB/Swiss-Prot;Acc:Q9M995]
15 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G07690.1); Ha. [Source:TAIR;Acc:AT1G54950]
16                                                                                                                                                                                      Proline-rich protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9FZ35]
17                                                                                                                                                                                     Domain of unknown function (DUF2431) [Source:TAIR;Acc:AT1G55790]
18                                                                                                                                                                                             At1g56580/F25P12_18 [Source:UniProtKB/TrEMBL;Acc:Q9FXB0]
   external_gene_name entrezgene_id
1                BXL2        837940
2                                NA
3                STP1        837667
4                            837742
5                LRX1        837756
6                           2745749
7              GSTU25        838289
8                BEE1        838421
9                FMO1        838508
10              LTPG1        839688
11                           839785
12                           840201
13         S-ACP-DES6        840977
14            AtGH9C1        841315
15                           841935
16               PRP1        841938
17                               NA
18                SVB        842112
 [ reached 'max' / getOption("max.print") -- omitted 82 rows ]

Investigations

Double carence en CO2 ambient et élevé

On s’interroge sur l’effet de la double carence fer et nitrate en CO2 ambiant et élevé. On ne l’avait pas fait car cela fait varer deux facteurs à la fois.

  (Intercept) groupcNF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cnf_2" "cnf_1" "cnf_3" "cNF_3" "cNF_2" "cNF_1"
    cnf_2     cnf_1     cnf_3     cNF_3     cNF_2     cNF_1 
1.0242524 1.0393358 1.0253221 0.9831632 0.9914864 0.9364401 

[1] "9070  genes DE"

  (Intercept) groupCNF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "Cnf_3" "Cnf_1" "Cnf_2" "CNF_1" "CNF_3" "CNF_2"
    Cnf_3     Cnf_1     Cnf_2     CNF_1     CNF_3     CNF_2 
0.9823882 1.0318759 1.0281336 1.0008911 0.9447685 1.0119428 

[1] "8309  genes DE"

   ensembl_gene_id
1        AT1G01720
2        AT1G01750
3        AT1G02575
4        AT1G02640
5        AT1G02850
6        AT1G03790
7        AT1G03870
8        AT1G04250
9        AT1G05650
10       AT1G05660
11       AT1G06120
12       AT1G07680
13       AT1G07690
14       AT1G07750
15       AT1G08080
16       AT1G08100
17       AT1G08290
18       AT1G08500
                                                                                                                                                                                                                                                                                                                                   description
1                                                                                                                                                                                                                                                                     NAC domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q39013]
2                                                                                                                                                                                                                                                                                   actin depolymerizing factor 11 [Source:TAIR;Acc:AT1G01750]
3                                                                                                                                                                                                                 unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G02570.1). [Source:TAIR;Acc:AT1G02575]
4                                                                                                                                                                                                                                                                        Probable beta-D-xylosidase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q94KD8]
5                                                                                                                                                                                                                                                                                 Beta-glucosidase 11 [Source:UniProtKB/Swiss-Prot;Acc:B3H5Q1]
6                                                                                                                                                                                                                                                        Zinc finger CCCH domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZWA1]
7                                                                                                                                                                                                                                                                                               At1g03870 [Source:UniProtKB/TrEMBL;Acc:B3LF88]
8                                                                                                                                                                                                                                                                      Auxin-responsive protein IAA17 [Source:UniProtKB/Swiss-Prot;Acc:P93830]
9                                                                                                                                                                                                                                                                                        F3F20.10 protein [Source:UniProtKB/TrEMBL;Acc:Q9SYK6]
10                                                                                                                                                                                                                                                                                       F3F20.11 protein [Source:UniProtKB/TrEMBL;Acc:Q9SYK7]
11                                                                                                                                                                                                                                                                  Delta-9 desaturase-like 3 protein [Source:UniProtKB/Swiss-Prot;Acc:Q9FPD5]
12                                                                                                                                                                                                                                                                                               F24B9.23 [Source:UniProtKB/TrEMBL;Acc:Q9LQP3]
13 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: root; CONTAINS InterPro DOMAIN/s: Orthoreovirus membrane fusion p10 (InterPro:IPR009854); BEST Arabidopsis thaliana pro /.../atch is: unknown protein (TAIR:AT1G54950.1); Ha. [Source:TAIR;Acc:AT1G07690]
14                                                                                                                                                                                                                                                                                     At1g07750/F24B9_13 [Source:UniProtKB/TrEMBL;Acc:Q9LQQ3]
15                                                                                                                                                                                                                                                                         Alpha carbonic anhydrase 7 [Source:UniProtKB/Swiss-Prot;Acc:Q8L817]
16                                                                                                                                                                                                                                                                                               NRT2 [Source:UniProtKB/TrEMBL;Acc:A0A178W7F7]
17                                                                                                                                                                                                                                                                           Zinc finger protein WIP3 [Source:UniProtKB/Swiss-Prot;Acc:Q9SGD1]
18                                                                                                                                                                                                                                                                          Early nodulin-like protein 18 [Source:UniProtKB/TrEMBL;Acc:O82083]
   external_gene_name entrezgene_id
1              NAC002        839265
2               ADF11        839281
3                          10723100
4                BXL2        837940
5              BGLU11        839435
6                 SOM        839408
7                FLA9        839384
8               IAA17        839568
9                            837072
10                           837073
11                           837121
12                           837281
13                           837282
14                           837290
15               ACA7        837326
16             NRT2.2        837328
17               WIP3        837349
18            ENODL18        837371
 [ reached 'max' / getOption("max.print") -- omitted 6632 rows ]

On trouve énormément de gènes, ce qui est cohérent car le nitrate et le fer pris séparément avaient déjà beaucoup d’effet.

DEG cNF et CNF avec un autre condition

On cherche à savoir si il n’y pas pas un soucis avec l’échantillon CNF, qui semble avoi très très peu de différences avec cNF. Aurait-on envoyé les mêmes tubes?

On ne voit que très peu de DEGs en comparant directement cNF et CNF, on cherche donc à savoir si on trouve le même nombre de DEGs quand on compare cNF - x et CNF -x, ce qui validerait l’hypothèse d’un transcriptôme quasi identique. On choisit ici par exemple \(x=\) cnF.

  (Intercept) groupcnF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "cnF_2" "cnF_1" "cnF_3"
    cNF_3     cNF_2     cNF_1     cnF_2     cnF_1     cnF_3 
0.9859482 0.9865531 0.9545113 1.0150637 1.0299591 1.0279646 
[1] "2803  genes DE"
  (Intercept) groupcnF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "cnF_2" "cnF_1" "cnF_3"
    CNF_1     CNF_3     CNF_2     cnF_2     cnF_1     cnF_3 
0.9885185 0.9468228 1.0077432 1.0150001 1.0207525 1.0211628 
[1] "1928  genes DE"

  (Intercept) groupcnf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "cnf_2" "cnf_1" "cnf_3"
    cNF_3     cNF_2     cNF_1     cnf_2     cnf_1     cnf_3 
0.9831632 0.9914864 0.9364401 1.0242524 1.0393358 1.0253221 
[1] "9069  genes DE"
  (Intercept) groupcnf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "cnf_2" "cnf_1" "cnf_3"
    CNF_1     CNF_3     CNF_2     cnf_2     cnf_1     cnf_3 
0.9883704 0.9318299 1.0000135 1.0208924 1.0390928 1.0198009 
[1] "8971  genes DE"

  (Intercept) groupcNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "cNf_1" "cNf_2" "cNf_3"
    cNF_3     cNF_2     cNF_1     cNf_1     cNf_2     cNf_3 
0.9844303 0.9894266 0.9466501 1.0201203 1.0475235 1.0118491 
[1] "7341  genes DE"
  (Intercept) groupcNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "cNf_1" "cNf_2" "cNf_3"
    CNF_1     CNF_3     CNF_2     cNf_1     cNf_2     cNf_3 
0.9891655 0.9317337 1.0004327 1.0190222 1.0502432 1.0094027 
[1] "7140  genes DE"

  (Intercept) groupCnF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "CnF_2" "CnF_1" "CnF_3"
    cNF_3     cNF_2     cNF_1     CnF_2     CnF_1     CnF_3 
0.9711423 0.9726028 0.9418377 1.0477020 1.0291049 1.0376104 
[1] "2855  genes DE"
  (Intercept) groupCnF
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "CnF_2" "CnF_1" "CnF_3"
    CNF_1     CNF_3     CNF_2     CnF_2     CnF_1     CnF_3 
0.9793780 0.9377198 0.9911882 1.0424709 1.0209230 1.0283201 
[1] "1811  genes DE"

  (Intercept) groupCnf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "Cnf_3" "Cnf_1" "Cnf_2"
    cNF_3     cNF_2     cNF_1     Cnf_3     Cnf_1     Cnf_2 
0.9967780 1.0011218 0.9585024 0.9781775 1.0283345 1.0370859 
[1] "8264  genes DE"
  (Intercept) groupCnf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "Cnf_3" "Cnf_1" "Cnf_2"
    CNF_1     CNF_3     CNF_2     Cnf_3     Cnf_1     Cnf_2 
1.0008911 0.9447685 1.0119428 0.9823882 1.0318759 1.0281336 
[1] "8309  genes DE"

  (Intercept) groupCNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "CNf_1" "CNf_3" "CNf_2"
    cNF_3     cNF_2     cNF_1     CNf_1     CNf_3     CNf_2 
0.9776759 0.9814592 0.9231468 1.0225871 1.0501686 1.0449624 
[1] "7401  genes DE"
  (Intercept) groupCNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "CNf_1" "CNf_3" "CNf_2"
    CNF_1     CNF_3     CNF_2     CNf_1     CNf_3     CNf_2 
0.9778008 0.9263592 0.9875116 1.0165429 1.0509593 1.0408262 
[1] "7531  genes DE"

[1] "Pourcentage des gènes DE qui ne sont pas partagés par les deux comparaisons :"
[1] 55.36533 23.39697 27.81213 57.43966 25.25306 27.71432

Il semble qu’il y ait quand même pas mal de différences entre ces transcriptomes, car quand on les compare au même troisième transcriptome on a une différence de 1000 gènes (1900 contre 2800). Le diagramme de Venn montre que ces gènes sont en partie différents. Les transcriptômes ont bien l’air différents. Si on prend un autre x :

  (Intercept) groupcNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "cNF_3" "cNF_2" "cNF_1" "cNf_1" "cNf_2" "cNf_3"
    cNF_3     cNF_2     cNF_1     cNf_1     cNf_2     cNf_3 
0.9844303 0.9894266 0.9466501 1.0201203 1.0475235 1.0118491 

[1] "7341  genes DE"

  (Intercept) groupcNf
1           1        0
2           1        0
3           1        0
4           1        1
5           1        1
6           1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

[1] "CNF_1" "CNF_3" "CNF_2" "cNf_1" "cNf_2" "cNf_3"
    CNF_1     CNF_3     CNF_2     cNf_1     cNf_2     cNf_3 
0.9891655 0.9317337 1.0004327 1.0190222 1.0502432 1.0094027 

[1] "7140  genes DE"

   ensembl_gene_id
1        AT1G01190
2        AT1G01720
3        AT1G02575
4        AT1G02850
5        AT1G03870
6        AT1G05660
7        AT1G05680
8        AT1G06120
9        AT1G07680
10       AT1G07690
11       AT1G09750
12       AT1G09932
13       AT1G10385
14       AT1G11545
15       AT1G12030
16       AT1G12080
17       AT1G12090
18       AT1G12200
                                                                                                                                                                                                                                                                                                                                   description
1                                                                                                                                                                                                                                                                                             CYP78A8 [Source:UniProtKB/TrEMBL;Acc:A0A178WIC4]
2                                                                                                                                                                                                                                                                     NAC domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q39013]
3                                                                                                                                                                                                                 unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G02570.1). [Source:TAIR;Acc:AT1G02575]
4                                                                                                                                                                                                                                                                                 Beta-glucosidase 11 [Source:UniProtKB/Swiss-Prot;Acc:B3H5Q1]
5                                                                                                                                                                                                                                                                                               At1g03870 [Source:UniProtKB/TrEMBL;Acc:B3LF88]
6                                                                                                                                                                                                                                                                                        F3F20.11 protein [Source:UniProtKB/TrEMBL;Acc:Q9SYK7]
7                                                                                                                                                                                                                                                                      Glycosyltransferase (Fragment) [Source:UniProtKB/TrEMBL;Acc:A0A0K1SBE8]
8                                                                                                                                                                                                                                                                   Delta-9 desaturase-like 3 protein [Source:UniProtKB/Swiss-Prot;Acc:Q9FPD5]
9                                                                                                                                                                                                                                                                                                F24B9.23 [Source:UniProtKB/TrEMBL;Acc:Q9LQP3]
10 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: root; CONTAINS InterPro DOMAIN/s: Orthoreovirus membrane fusion p10 (InterPro:IPR009854); BEST Arabidopsis thaliana pro /.../atch is: unknown protein (TAIR:AT1G54950.1); Ha. [Source:TAIR;Acc:AT1G07690]
11                                                                                                                                                                                                                                                                             Aspartyl protease AED3 [Source:UniProtKB/Swiss-Prot;Acc:O04496]
12                                                                                                                                                                                                                                                                 Phosphoglycerate mutase family protein [Source:UniProtKB/TrEMBL;Acc:Q8GWG7]
13                                                                                                                                                                                                                                                                   Exocyst complex component EXO84A [Source:UniProtKB/Swiss-Prot;Acc:F4I4B6]
14                                                                                                                                                                                                                                                          Xyloglucan endotransglucosylase/hydrolase [Source:UniProtKB/TrEMBL;Acc:A0A178W0W2]
15                                                                                                                                                                                                                                                                                              At1g12030 [Source:UniProtKB/TrEMBL;Acc:O65376]
16                                                                                                                                                                                                                                                                                              At1g12080 [Source:UniProtKB/TrEMBL;Acc:O65370]
17                                                                                                                                                                                                                                                                                                ELP [Source:UniProtKB/TrEMBL;Acc:A0A178W1A4]
18                                                                                                                                                                                                                                                                    Flavin-containing monooxygenase [Source:UniProtKB/TrEMBL;Acc:A0A178W1K3]
   external_gene_name entrezgene_id
1             CYP78A8        839233
2              NAC002        839265
3                          10723100
4              BGLU11        839435
5                FLA9        839384
6                            837073
7             UGT74E2        837075
8                            837121
9                            837281
10                           837282
11               AED3        837504
12                           837526
13             EXO84A        837578
14               XTH8        837698
15                           837755
16                           837760
17                ELP        837761
18                           837773
 [ reached 'max' / getOption("max.print") -- omitted 6047 rows ]

On va faire les corrélations d’expression entre ces deux conditions.

[1] 0.9938199 0.9906937 0.9810858 0.9860430 0.9921428 0.9860068

cNF et CNF semblent bien plus proches entre eux que cNF ne l’est avec tous les autres.

 

A work by Océane Cassan

oceane.cassan@supagro.fr